std::vector<GeoLib::PointWithID*> MshEditor::getSurfaceNodes(const MeshLib::Mesh &mesh, const double *dir)
{
INFO ("Extracting surface nodes...");
const std::vector<MeshLib::Element*> all_elements (mesh.getElements());
const std::vector<MeshLib::Node*> all_nodes (mesh.getNodes());
std::vector<MeshLib::Element*> sfc_elements;
get2DSurfaceElements(all_elements, sfc_elements, dir, mesh.getDimension());
std::vector<MeshLib::Node*> sfc_nodes;
std::vector<unsigned> node_id_map(mesh.getNNodes());
get2DSurfaceNodes(all_nodes, sfc_nodes, sfc_elements, node_id_map);
const unsigned nElements (sfc_elements.size());
for (unsigned i=0; i<nElements; ++i)
delete sfc_elements[i];
const size_t nNodes (sfc_nodes.size());
std::vector<GeoLib::PointWithID*> surface_pnts(nNodes);
for (unsigned i=0; i<nNodes; ++i)
{
surface_pnts[i] = new GeoLib::PointWithID(sfc_nodes[i]->getCoords(), sfc_nodes[i]->getID());
delete sfc_nodes[i];
}
return surface_pnts;
}
void LayeredVolume::addLayerToMesh(const MeshLib::Mesh &dem_mesh, unsigned layer_id, GeoLib::Raster const& raster)
{
const std::size_t nNodes (dem_mesh.getNNodes());
const std::vector<MeshLib::Node*> &nodes (dem_mesh.getNodes());
const std::size_t node_id_offset (_nodes.size());
const std::size_t last_layer_node_offset (node_id_offset-nNodes);
for (std::size_t i=0; i<nNodes; ++i)
_nodes.push_back(getNewLayerNode(*nodes[i], *_nodes[last_layer_node_offset + i], raster, _nodes.size()));
const std::vector<MeshLib::Element*> &layer_elements (dem_mesh.getElements());
for (MeshLib::Element* elem : layer_elements)
{
if (elem->getGeomType() == MeshLib::MeshElemType::TRIANGLE)
{
std::array<MeshLib::Node*,3> tri_nodes = {{ _nodes[node_id_offset+elem->getNodeIndex(0)],
_nodes[node_id_offset+elem->getNodeIndex(1)],
_nodes[node_id_offset+elem->getNodeIndex(2)] }};
_elements.push_back(new MeshLib::Tri(tri_nodes, layer_id));
}
else if (elem->getGeomType() == MeshLib::MeshElemType::QUAD)
{
std::array<MeshLib::Node*,4> quad_nodes = {{ _nodes[node_id_offset+elem->getNodeIndex(0)],
_nodes[node_id_offset+elem->getNodeIndex(1)],
_nodes[node_id_offset+elem->getNodeIndex(2)],
_nodes[node_id_offset+elem->getNodeIndex(3)] }};
_elements.push_back(new MeshLib::Quad(quad_nodes, layer_id));
}
}
}
int main (int argc, char* argv[])
{
LOGOG_INITIALIZE();
logog::Cout* logog_cout (new logog::Cout);
BaseLib::LogogSimpleFormatter *custom_format (new BaseLib::LogogSimpleFormatter);
logog_cout->SetFormatter(*custom_format);
TCLAP::CmdLine cmd("Converts VTK mesh into OGS mesh.", ' ', "0.1");
TCLAP::ValueArg<std::string> mesh_in("i", "mesh-input-file",
"the name of the file containing the input mesh", true,
"", "file name of input mesh");
cmd.add(mesh_in);
TCLAP::ValueArg<std::string> mesh_out("o", "mesh-output-file",
"the name of the file the mesh will be written to", true,
"", "file name of output mesh");
cmd.add(mesh_out);
cmd.parse(argc, argv);
MeshLib::Mesh* mesh (FileIO::BoostVtuInterface::readVTUFile(mesh_in.getValue()));
INFO("Mesh read: %d nodes, %d elements.", mesh->getNNodes(), mesh->getNElements());
FileIO::Legacy::MeshIO meshIO;
meshIO.setMesh(mesh);
meshIO.writeToFile(mesh_out.getValue());
delete custom_format;
delete logog_cout;
LOGOG_SHUTDOWN();
return 0;
}
void MeshSurfaceExtraction::getSurfaceAreaForNodes(const MeshLib::Mesh &mesh, std::vector<double> &node_area_vec)
{
if (mesh.getDimension() == 2)
{
double total_area (0);
// for each node, a vector containing all the element idget every element
const std::vector<MeshLib::Node*> &nodes = mesh.getNodes();
const size_t nNodes ( mesh.getNNodes() );
node_area_vec.reserve(nNodes);
for (size_t n=0; n<nNodes; ++n)
{
double node_area (0);
std::vector<MeshLib::Element*> conn_elems = nodes[n]->getElements();
const size_t nConnElems (conn_elems.size());
for (size_t i=0; i<nConnElems; ++i)
{
const MeshLib::Element* elem (conn_elems[i]);
const unsigned nElemParts = (elem->getGeomType() == MeshElemType::TRIANGLE) ? 3 : 4;
const double area = conn_elems[i]->getContent() / nElemParts;
node_area += area;
total_area += area;
}
node_area_vec.push_back(node_area);
}
INFO ("Total surface Area: %f", total_area);
}
else
ERR ("Error in MeshSurfaceExtraction::getSurfaceAreaForNodes() - Given mesh is no surface mesh (dimension != 2).");
}
void LayeredVolume::addLayerBoundaries(const MeshLib::Mesh &layer, std::size_t nLayers)
{
const unsigned nLayerBoundaries (nLayers-1);
const std::size_t nNodes (layer.getNNodes());
const std::vector<MeshLib::Element*> &layer_elements (layer.getElements());
for (MeshLib::Element* elem : layer_elements)
{
const std::size_t nElemNodes (elem->getNBaseNodes());
for (unsigned i=0; i<nElemNodes; ++i)
if (elem->getNeighbor(i) == nullptr)
for (unsigned j=0; j<nLayerBoundaries; ++j)
{
const std::size_t offset (j*nNodes);
MeshLib::Node* n0 = _nodes[offset + elem->getNodeIndex(i)];
MeshLib::Node* n1 = _nodes[offset + elem->getNodeIndex((i+1)%nElemNodes)];
MeshLib::Node* n2 = _nodes[offset + nNodes + elem->getNodeIndex((i+1)%nElemNodes)];
MeshLib::Node* n3 = _nodes[offset + nNodes + elem->getNodeIndex(i)];
if (MathLib::Vector3(*n1, *n2).getLength() > std::numeric_limits<double>::epsilon())
{
const std::array<MeshLib::Node*,3> tri_nodes = {{ n0, n2, n1 }};
_elements.push_back(new MeshLib::Tri(tri_nodes, nLayers+1+j));
}
if (MathLib::Vector3(*n0, *n3).getLength() > std::numeric_limits<double>::epsilon())
{
const std::array<MeshLib::Node*,3> tri_nodes = {{ n0, n3, n2 }};
_elements.push_back(new MeshLib::Tri(tri_nodes, nLayers+1+j));
}
}
}
}
void testZCoords2D(MeshLib::Mesh const& input, MeshLib::Mesh const& output, double height)
{
std::size_t const nNodes (input.getNNodes());
for (std::size_t i=0; i<nNodes; ++i)
{
ASSERT_EQ((*input.getNode(i))[2], (*output.getNode(i))[2]);
ASSERT_EQ((*input.getNode(i))[2] + height, (*output.getNode(nNodes+i))[2]);
}
}
std::vector<GeoLib::Point*> MeshSurfaceExtraction::getSurfaceNodes(const MeshLib::Mesh &mesh, const MathLib::Vector3 &dir, double angle)
{
INFO ("Extracting surface nodes...");
std::vector<MeshLib::Element*> sfc_elements;
get2DSurfaceElements(mesh.getElements(), sfc_elements, dir, angle, mesh.getDimension());
std::vector<MeshLib::Node*> sfc_nodes;
std::vector<std::size_t> node_id_map(mesh.getNNodes());
get2DSurfaceNodes(sfc_nodes, mesh.getNNodes(), sfc_elements, node_id_map);
for (auto e : sfc_elements)
delete e;
const std::size_t nNodes (sfc_nodes.size());
std::vector<GeoLib::Point*> surface_pnts(nNodes);
for (std::size_t i=0; i<nNodes; ++i)
{
surface_pnts[i] = new GeoLib::Point(*(sfc_nodes[i]), sfc_nodes[i]->getID());
delete sfc_nodes[i];
}
return surface_pnts;
}
SparsityPattern
computeSparsityPattern(LocalToGlobalIndexMap const& dof_table,
MeshLib::Mesh const& mesh
)
{
MeshLib::NodeAdjacencyTable node_adjacency_table;
node_adjacency_table.createTable(mesh.getNodes());
// A mapping mesh node id -> global indices
// It acts as a cache for dof table queries.
std::vector<std::vector<GlobalIndexType> > global_idcs;
global_idcs.reserve(mesh.getNNodes());
for (std::size_t n=0; n<mesh.getNNodes(); ++n)
{
MeshLib::Location l(mesh.getID(), MeshLib::MeshItemType::Node, n);
global_idcs.push_back(dof_table.getGlobalIndices(l));
}
SparsityPattern sparsity_pattern(dof_table.dofSize());
// Map adjacent mesh nodes to "adjacent global indices".
for (std::size_t n=0; n<mesh.getNNodes(); ++n)
{
auto const& node_ids = node_adjacency_table.getAdjacentNodes(n);
for (auto an : node_ids) {
auto const& row_ids = global_idcs[an];
auto const num_components = row_ids.size();
for (auto r : row_ids) {
// Each component leads to an entry in the row.
// For the sparsity pattern only the number of entries are needed.
sparsity_pattern[r] += num_components;
}
}
}
return sparsity_pattern;
}
TEST(MeshLib, Duplicate)
{
MeshLib::Mesh* mesh (MeshLib::MeshGenerator::generateRegularQuadMesh(10, 5, 1));
std::vector<MeshLib::Node*> new_nodes (MeshLib::copyNodeVector(mesh->getNodes()));
std::vector<MeshLib::Element*> new_elements (MeshLib::copyElementVector(mesh->getElements(), new_nodes));
MeshLib::Mesh new_mesh ("new", new_nodes, new_elements);
ASSERT_EQ (mesh->getNElements(), new_mesh.getNElements());
ASSERT_EQ (mesh->getNNodes(), new_mesh.getNNodes());
std::vector<std::size_t> del_idx(1,1);
MeshLib::removeMeshNodes(*mesh, del_idx);
ASSERT_EQ (mesh->getNElements(), new_mesh.getNElements()-2);
ASSERT_EQ (mesh->getNNodes(), new_mesh.getNNodes()-2);
ASSERT_DOUBLE_EQ (4.0, MathLib::sqrDist(*mesh->getNode(0), *new_mesh.getNode(0)));
ASSERT_DOUBLE_EQ (0.0, MathLib::sqrDist(*mesh->getNode(0), *new_mesh.getNode(2)));
ASSERT_DOUBLE_EQ (4.0, MathLib::sqrDist(*mesh->getElement(0)->getNode(0), *new_mesh.getElement(0)->getNode(0)));
ASSERT_DOUBLE_EQ (0.0, MathLib::sqrDist(*mesh->getElement(0)->getNode(0), *new_mesh.getElement(2)->getNode(0)));
}
TEST(MeshLib, ElementStatus)
{
const unsigned width (100);
const unsigned elements_per_side (20);
MeshLib::Mesh* mesh (MeshLib::MeshGenerator::generateRegularQuadMesh(width, elements_per_side));
MeshLib::ElementStatus status(mesh);
const std::vector<MeshLib::Element*> elements (mesh->getElements());
for (unsigned i=0; i<elements_per_side; ++i)
{
for (unsigned j=0; j<elements_per_side; ++j)
elements[i*elements_per_side + j]->setValue(i);
}
// all elements active
ASSERT_EQ (elements.size(), status.getNActiveElements());
// all nodes active
ASSERT_EQ (mesh->getNNodes(), status.getNActiveNodes());
// set material 1 to false
status.setMaterialStatus(1, false);
ASSERT_EQ (elements.size()-elements_per_side, status.getNActiveElements());
// set material 1 to false (again)
status.setMaterialStatus(1, false);
ASSERT_EQ (elements.size()-elements_per_side, status.getNActiveElements());
// set material 0 to false
status.setMaterialStatus(0, false);
ASSERT_EQ (elements.size()-(2*elements_per_side), status.getNActiveElements());
// active elements
std::vector<std::size_t> active_elements (status.getActiveElements());
ASSERT_EQ (active_elements.size(), status.getNActiveElements());
// active nodes
std::vector<std::size_t> active_nodes (status.getActiveNodes());
ASSERT_EQ (active_nodes.size(), status.getNActiveNodes());
// set element 1 to false (yet again)
status.setElementStatus(1, false);
status.getElementStatus(1);
ASSERT_EQ (elements.size()-(2*elements_per_side), status.getNActiveElements());
ASSERT_EQ (mesh->getNNodes()-(2*(elements_per_side+1)), status.getNActiveNodes());
// set element 1 to true
status.setElementStatus(1, true);
ASSERT_EQ (elements.size()-(2*elements_per_side)+1, status.getNActiveElements());
ASSERT_EQ (mesh->getNNodes()-(2*(elements_per_side+1))+4, status.getNActiveNodes());
ASSERT_EQ(status.getElementStatus(1), true);
std::vector<std::size_t> active_elements_at_node (status.getActiveElementsAtNode(2));
ASSERT_EQ(1u, active_elements_at_node.size());
active_elements_at_node = status.getActiveElementsAtNode(22);
ASSERT_EQ(1u, active_elements_at_node.size());
active_elements_at_node = status.getActiveElementsAtNode(44);
ASSERT_EQ(2u, active_elements_at_node.size());
active_elements_at_node = status.getActiveElementsAtNode(102);
ASSERT_EQ(4u, active_elements_at_node.size());
status.setAll(true);
ASSERT_EQ(elements.size(), status.getNActiveElements());
ASSERT_EQ(mesh->getNNodes(), status.getNActiveNodes());
status.setAll(false);
ASSERT_EQ(0u, status.getNActiveElements());
ASSERT_EQ(0u, status.getNActiveNodes());
}
int main (int argc, char* argv[])
{
LOGOG_INITIALIZE();
logog::Cout* logog_cout (new logog::Cout);
BaseLib::LogogSimpleFormatter *custom_format (new BaseLib::LogogSimpleFormatter);
logog_cout->SetFormatter(*custom_format);
TCLAP::CmdLine cmd("Add EMI data as a scalar cell array to a 2d mesh.", ' ', "0.1");
// I/O params
TCLAP::ValueArg<std::string> poly_out("o", "polydata-output-file",
"the name of the file the data will be written to", true,
"", "file name of polydata file");
cmd.add(poly_out);
TCLAP::ValueArg<std::string> csv_in("i", "csv-input-file",
"csv-file containing EMI data", true,
"", "name of the csv input file");
cmd.add(csv_in);
TCLAP::ValueArg<std::string> dem_in("s", "DEM-file",
"Surface DEM for mapping ERT data", false,
"", "file name of the Surface DEM");
cmd.add(dem_in);
cmd.parse(argc, argv);
MeshLib::Mesh* mesh (nullptr);
if (dem_in.isSet())
{
mesh = FileIO::VtuInterface::readVTUFile(dem_in.getValue());
if (mesh == nullptr)
{
ERR ("Error reading mesh file.");
return -2;
}
if (mesh->getDimension() != 2)
{
ERR ("This utility can handle only 2d meshes at this point.");
delete mesh;
return -3;
}
INFO("Surface mesh read: %d nodes, %d elements.", mesh->getNNodes(), mesh->getNElements());
}
GeoLib::GEOObjects geo_objects;
FileIO::XmlGmlInterface xml(geo_objects);
//std::vector<GeoLib::Polyline*> *lines = new std::vector<GeoLib::Polyline*>;
std::array<char, 2> dipol = {{ 'H', 'V' }};
std::array<char,3> const regions = {{'A', 'B', 'C'}};
for (std::size_t j=0; j<dipol.size(); ++j)
{
std::vector<GeoLib::Point*> *points = new std::vector<GeoLib::Point*>;
for (std::size_t i=0; i<regions.size(); ++i)
{
//std::size_t const start_idx (points->size());
getPointsFromFile(*points, csv_in.getValue(), dipol[j], regions[i]);
//std::size_t const end_idx (points->size());
//GeoLib::Polyline* line = new GeoLib::Polyline(*points);
//for (std::size_t j=start_idx; j<end_idx; ++j)
// line->addPoint(j);
//lines->push_back(line);
}
std::string geo_name (std::string("EMI Data ").append(1,dipol[j]));
geo_objects.addPointVec(points, geo_name);
//geo_objects.addPolylineVec(lines, geo_name);
if (mesh != nullptr)
{
GeoMapper mapper(geo_objects, geo_name);
mapper.mapOnMesh(mesh);
}
xml.setNameForExport(geo_name);
std::string const output_name = poly_out.getValue() + "_" + dipol[j] + ".gml";
xml.writeToFile(output_name);
std::vector<double> emi;
for (std::size_t i=0; i<regions.size(); ++i)
getMeasurements(emi, csv_in.getValue(), dipol[j], regions[i]);
writeMeasurementsToFile(emi, poly_out.getValue(), dipol[j]);
std::for_each(points->begin(), points->end(), std::default_delete<GeoLib::Point>());
delete points;
}
delete mesh;
delete custom_format;
delete logog_cout;
LOGOG_SHUTDOWN();
return 0;
}
int main (int argc, char* argv[])
{
LOGOG_INITIALIZE();
logog::Cout* logog_cout (new logog::Cout);
BaseLib::LogogSimpleFormatter *custom_format (new BaseLib::LogogSimpleFormatter);
logog_cout->SetFormatter(*custom_format);
TCLAP::CmdLine cmd("Edit material IDs of mesh elements.", ' ', "0.1");
TCLAP::SwitchArg replaceArg("r", "replace", "replace material IDs", false);
TCLAP::SwitchArg condenseArg("c", "condense", "condense material IDs", false);
TCLAP::SwitchArg specifyArg("s", "specify", "specify material IDs by element types (-e)", false);
std::vector<TCLAP::Arg*> vec_xors;
vec_xors.push_back(&replaceArg);
vec_xors.push_back(&condenseArg);
vec_xors.push_back(&specifyArg);
cmd.xorAdd(vec_xors);
TCLAP::ValueArg<std::string> mesh_in("i", "mesh-input-file",
"the name of the file containing the input mesh", true,
"", "file name");
cmd.add(mesh_in);
TCLAP::ValueArg<std::string> mesh_out("o", "mesh-output-file",
"the name of the file the mesh will be written to", true,
"", "file name");
cmd.add(mesh_out);
TCLAP::MultiArg<unsigned> matIDArg("m", "current-material-id",
"current material id to be replaced", false, "number");
cmd.add(matIDArg);
TCLAP::ValueArg<unsigned> newIDArg("n", "new-material-id",
"new material id", false, 0, "number");
cmd.add(newIDArg);
std::vector<std::string> eleList(MeshLib::getMeshElemTypeStringsShort());
TCLAP::ValuesConstraint<std::string> allowedVals(eleList);
TCLAP::ValueArg<std::string> eleTypeArg("e", "element-type",
"element type", false, "", &allowedVals);
cmd.add(eleTypeArg);
cmd.parse(argc, argv);
if (!replaceArg.isSet() && !condenseArg.isSet() && !specifyArg.isSet()) {
INFO("Please select editing mode: -r or -c or -s");
return 0;
} else if (replaceArg.isSet() && condenseArg.isSet()) {
INFO("Please select only one editing mode: -r or -c or -s");
return 0;
} else if (replaceArg.isSet()) {
if (!matIDArg.isSet() || !newIDArg.isSet()) {
INFO("current and new material IDs must be provided for replacement");
return 0;
}
} else if (specifyArg.isSet()) {
if (!eleTypeArg.isSet() || !newIDArg.isSet()) {
INFO("element type and new material IDs must be provided to specify elements");
return 0;
}
}
MeshLib::Mesh* mesh (FileIO::readMeshFromFile(mesh_in.getValue()));
INFO("Mesh read: %d nodes, %d elements.", mesh->getNNodes(), mesh->getNElements());
if (condenseArg.isSet()) {
INFO("Condensing material ID...");
MeshLib::ElementValueModification::condense(*mesh);
} else if (replaceArg.isSet()) {
INFO("Replacing material ID...");
const auto vecOldID = matIDArg.getValue();
const unsigned newID = newIDArg.getValue();
for (auto oldID : vecOldID) {
INFO("%d -> %d", oldID, newID);
MeshLib::ElementValueModification::replace(*mesh, oldID, newID, true);
}
} else if (specifyArg.isSet()) {
INFO("Specifying material ID...");
const std::string eleTypeName(eleTypeArg.getValue());
const MeshLib::MeshElemType eleType = MeshLib::String2MeshElemType(eleTypeName);
const unsigned newID = newIDArg.getValue();
unsigned cnt = MeshLib::ElementValueModification::setByElementType(*mesh, eleType, newID);
INFO("updated %d elements", cnt);
}
// write into a file
FileIO::writeMeshToFile(*mesh, mesh_out.getValue());
delete custom_format;
delete logog_cout;
LOGOG_SHUTDOWN();
return 0;
}
int main (int argc, char* argv[])
{
LOGOG_INITIALIZE();
logog::Cout* logog_cout (new logog::Cout);
BaseLib::LogogSimpleFormatter *custom_format (new BaseLib::LogogSimpleFormatter);
logog_cout->SetFormatter(*custom_format);
TCLAP::CmdLine cmd("Remove mesh elements.", ' ', "0.1");
TCLAP::ValueArg<std::string> mesh_in("i", "mesh-input-file",
"the name of the file containing the input mesh", true,
"", "file name of input mesh");
cmd.add(mesh_in);
TCLAP::ValueArg<std::string> mesh_out("o", "mesh-output-file",
"the name of the file the mesh will be written to", true,
"", "file name of output mesh");
cmd.add(mesh_out);
TCLAP::SwitchArg zveArg("z", "zero-volume", "remove zero volume elements", false);
cmd.add(zveArg);
TCLAP::MultiArg<std::string> eleTypeArg("t", "element-type",
"element type to be removed", false, "element type");
cmd.add(eleTypeArg);
TCLAP::MultiArg<unsigned> matIDArg("m", "material-id",
"material id", false, "material id");
cmd.add(matIDArg);
cmd.parse(argc, argv);
MeshLib::Mesh* mesh (FileIO::readMeshFromFile(mesh_in.getValue()));
INFO("Mesh read: %d nodes, %d elements.", mesh->getNNodes(), mesh->getNElements());
// search elements IDs to be removed
std::vector<std::size_t> vec_elementIDs_removed;
if (zveArg.isSet()) {
std::vector<std::size_t> vec_matched = searchByZeroContent(mesh->getElements());
updateUnion(vec_matched, vec_elementIDs_removed);
INFO("%d zero volume elements found.", vec_matched.size());
}
if (eleTypeArg.isSet()) {
std::vector<std::string> eleTypeNames = eleTypeArg.getValue();
for (auto typeName : eleTypeNames) {
MeshElemType type = String2MeshElemType(typeName);
if (type == MeshElemType::INVALID) continue;
std::vector<std::size_t> vec_matched = searchByElementType(mesh->getElements(), type);
updateUnion(vec_matched, vec_elementIDs_removed);
INFO("%d %s elements found.", vec_matched.size(), typeName.c_str());
}
}
if (matIDArg.isSet()) {
std::vector<unsigned> vec_matID = matIDArg.getValue();
for (auto matID : vec_matID) {
std::vector<std::size_t> vec_matched = searchByMaterialID(mesh->getElements(), matID);
updateUnion(vec_matched, vec_elementIDs_removed);
INFO("%d elements with material ID %d found.", vec_matched.size(), matID);
}
}
// remove the elements
INFO("Removing total %d elements...", vec_elementIDs_removed.size());
std::vector<MeshLib::Element*> tmp_eles = excludeElements(mesh->getElements(), vec_elementIDs_removed);
INFO("%d elements remained.", tmp_eles.size());
std::vector<MeshLib::Node*> new_nodes;
std::vector<MeshLib::Element*> new_eles;
copyNodesElements(mesh->getNodes(), tmp_eles, new_nodes, new_eles);
// create a new mesh object. Unsued nodes are removed while construction
MeshLib::Mesh* new_mesh(new MeshLib::Mesh(mesh->getName(), new_nodes, new_eles));
// write into a file
FileIO::Legacy::MeshIO meshIO;
meshIO.setMesh(new_mesh);
meshIO.writeToFile(mesh_out.getValue());
delete custom_format;
delete logog_cout;
LOGOG_SHUTDOWN();
return 0;
}